Contacts of the helix formed by residues 450 - 466 (chain A) in PDB entry 2VGB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 450 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A SER* 3.4 9.0 + - - +
449A ARG* 1.3 76.1 - - - +
451A PRO* 1.3 74.8 - - - +
452A THR* 3.1 28.9 + - - -
453A GLU* 3.0 22.0 + - + +
454A VAL* 3.0 11.9 + - - +
479A ARG* 5.0 7.4 + - - -
483A LEU* 4.0 9.0 - - - +
563A GLY 5.1 2.9 - - - +
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Residues in contact with PRO 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ARG 3.2 10.5 - - - +
450A ASP* 1.3 90.9 - - - +
452A THR* 1.3 51.6 + - - +
454A VAL* 3.3 10.1 + - + +
455A THR* 2.7 38.6 + - - -
563A GLY 6.1 1.6 - - - +
564A TYR* 6.4 0.4 - - - -
565A THR 3.9 12.6 - - - +
566A ASN* 4.3 7.4 - - + -
551B LEU* 4.5 9.6 - - + -
570B VAL* 3.8 24.5 - - + +
571B LEU 6.4 0.2 - - - -
572B SER* 6.1 2.0 - - - +
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Residues in contact with THR 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ASP* 3.0 19.4 + - - -
451A PRO* 1.3 74.1 - - - +
453A GLU* 1.3 66.4 + - - +
455A THR* 3.3 4.8 + - - -
456A ALA* 3.0 21.5 + - - +
479A ARG* 5.2 2.7 - - + -
480A SER* 3.6 31.2 - - - +
483A LEU* 3.5 17.9 - - + -
563A GLY* 4.2 15.4 + - - -
565A THR* 3.7 27.5 + - + +
580A FBP 5.6 1.6 - - - +
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Residues in contact with GLU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER* 3.6 29.4 + - - +
450A ASP* 3.0 17.5 + - + +
452A THR* 1.3 76.9 - - - +
454A VAL* 1.3 63.6 + - - +
456A ALA* 3.0 16.5 + - - +
457A ILE* 3.0 17.0 + - - +
479A ARG* 5.6 1.8 + - - +
483A LEU* 3.6 32.1 - - + +
486A ARG* 4.3 13.7 + - - -
487A TYR* 2.8 35.9 + - - -
465B LYS* 3.9 5.5 + - - -
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Residues in contact with VAL 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER 3.9 22.0 - - - +
449A ARG 4.4 1.1 - - - +
450A ASP 3.0 23.1 - - - +
451A PRO* 3.5 8.3 - - + +
453A GLU* 1.3 75.7 - - + +
455A THR* 1.3 60.3 + - - +
457A ILE* 3.4 9.6 - - - +
458A GLY 3.3 14.7 + - - -
462B ALA* 3.3 43.0 - - + +
465B LYS* 4.7 5.6 - - + -
466B CYS* 3.8 18.2 - - + -
551B LEU* 4.7 2.2 - - + -
553B ILE* 4.3 0.4 - - + -
570B VAL* 3.8 17.0 - - + -
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Residues in contact with THR 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A PRO 2.7 22.1 + - - -
452A THR 3.7 4.5 - - - -
454A VAL* 1.3 73.9 - - - +
456A ALA* 1.3 56.6 + - - +
458A GLY* 3.2 1.7 + - - -
459A ALA* 2.8 34.1 + - - +
555A VAL* 4.1 13.0 - - + -
565A THR* 4.5 5.4 - - - -
566A ASN* 3.3 21.4 + - - +
567A ILE 3.5 37.7 - - - +
568A MET* 4.0 11.0 - - + +
568B MET* 4.7 7.0 - - + -
570B VAL* 3.8 8.9 - - - +
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Residues in contact with ALA 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A THR* 3.0 13.3 + - + +
453A GLU* 3.1 10.8 - - - +
455A THR* 1.3 75.3 - - - +
457A ILE* 1.3 60.2 + - - +
459A ALA* 2.8 5.0 + - - +
460A VAL* 2.8 31.9 + - - +
480A SER 5.3 0.9 - - - +
483A LEU* 3.8 35.9 - - + +
484A LEU* 3.7 18.4 - - + +
487A TYR* 4.6 2.2 - - + -
555A VAL* 5.8 2.2 - - - +
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Residues in contact with ILE 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A PHE* 4.3 14.1 - - + -
442A ARG* 4.2 16.4 - - + -
453A GLU 3.0 9.4 + - - +
454A VAL 3.4 13.0 - - - +
456A ALA* 1.3 78.5 - - - +
458A GLY* 1.3 60.7 + - - +
460A VAL* 3.4 3.6 + - - +
461A GLU* 2.9 29.3 + - - +
487A TYR* 3.8 35.4 - - + -
461B GLU* 3.0 37.5 - - + +
462B ALA* 4.6 0.9 - - - -
465B LYS* 3.9 36.8 - - + -
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Residues in contact with GLY 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A VAL 3.3 6.5 + - - -
455A THR 3.2 5.6 + - - -
456A ALA 3.1 1.0 - - - -
457A ILE* 1.3 84.5 - - - +
459A ALA* 1.3 55.8 + - - +
461A GLU* 3.2 6.1 + - - +
462A ALA* 2.8 29.5 + - - +
568A MET* 4.2 6.5 - - - -
458B GLY* 3.8 24.5 - - - -
461B GLU* 4.5 2.2 - - - -
462B ALA* 4.6 3.6 - - - -
568B MET* 4.9 4.0 - - - -
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Residues in contact with ALA 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A THR 2.8 13.6 + - - +
456A ALA 2.8 7.8 + - - +
458A GLY* 1.3 74.7 - - - +
460A VAL* 1.3 66.2 + - - +
462A ALA* 3.2 2.9 + - - +
463A ALA* 2.9 24.5 + - - +
471A ILE* 4.5 4.0 - - + -
484A LEU* 3.7 17.5 - - + -
553A ILE* 4.0 9.2 - - + +
555A VAL* 3.7 20.6 - - + -
568A MET* 3.9 18.1 - - + -
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Residues in contact with VAL 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE* 3.8 17.7 - - + -
456A ALA 2.8 22.6 + - - +
457A ILE 3.7 5.2 - - - +
459A ALA* 1.3 71.9 - - - +
461A GLU* 1.3 62.1 + - - +
463A ALA* 3.2 8.4 + - - +
464A PHE* 3.0 46.4 + - + -
471A ILE* 4.3 2.2 - - + -
484A LEU* 3.8 22.0 - - + +
487A TYR* 3.9 18.8 - - + +
489A PRO* 3.6 28.7 - - + -
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Residues in contact with GLU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE* 3.8 16.0 - - + -
457A ILE 2.9 18.2 + - - +
458A GLY 3.2 4.5 + - - +
460A VAL* 1.3 77.6 - - - +
462A ALA* 1.3 62.5 + - - +
464A PHE* 3.2 8.1 + - - +
465A LYS* 3.2 19.8 + - - +
442B ARG* 3.7 26.2 + - - -
457B ILE* 3.1 43.8 - - + +
458B GLY* 4.5 0.2 - - - -
461B GLU* 2.7 45.3 - - + +
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Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A GLY 2.8 15.4 + - - +
459A ALA 3.6 4.5 - - - +
461A GLU* 1.3 77.5 - - - +
463A ALA* 1.3 63.4 + - - +
465A LYS* 3.1 12.1 + - - -
466A CYS* 3.4 5.5 + - - -
553A ILE* 3.9 14.4 - - + -
568A MET* 4.0 17.3 - - + -
454B VAL* 3.4 47.4 - - + +
457B ILE* 4.9 0.2 - - - -
458B GLY* 4.6 2.2 - - - -
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Residues in contact with ALA 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A ALA 2.9 12.8 + - - +
460A VAL* 3.3 10.3 - - - +
462A ALA* 1.3 76.7 - - - +
464A PHE* 1.3 64.4 + - + +
465A LYS 3.2 0.3 + - - -
466A CYS 3.2 1.7 + - - -
467A CYS* 3.0 5.0 + - - -
468A ALA* 3.0 46.0 + - + -
471A ILE* 4.1 18.4 - - + -
489A PRO* 5.3 2.5 - - + -
490A ARG 6.1 0.2 - - - +
491A ALA* 4.3 9.0 - - + +
553A ILE* 4.0 7.4 - - + +
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Residues in contact with PHE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A HIS* 4.0 28.3 - + + -
435A ARG 5.8 0.2 - - - -
438A PHE* 3.6 37.2 - + + -
460A VAL* 3.0 42.9 + - + -
461A GLU* 3.2 12.1 + - - +
463A ALA* 1.3 78.5 - - + +
465A LYS* 1.3 61.9 + - - +
466A CYS 3.2 1.0 + - - -
467A CYS* 3.4 13.9 + - - +
488A ARG 3.8 19.5 - - - -
489A PRO* 4.3 1.8 - - + -
490A ARG* 4.0 25.4 - - + -
447B LEU* 4.7 8.0 - - - +
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Residues in contact with LYS 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A GLU* 3.2 11.5 + - - +
462A ALA 3.1 11.4 + - - +
464A PHE* 1.3 76.9 - - - +
466A CYS* 1.3 56.2 + - - +
467A CYS 3.6 0.2 - - - -
442B ARG* 5.4 1.2 + - - +
445B ALA* 3.9 13.7 + - - +
446B PRO 2.6 27.6 + - - +
447B LEU* 3.9 12.9 - - + +
448B SER* 2.9 51.7 + - - +
453B GLU* 4.2 8.5 + - - -
454B VAL* 4.4 11.7 - - + -
457B ILE* 4.1 33.6 - - + +
487B TYR* 3.3 26.1 + - - -
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Residues in contact with CYS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ALA 3.4 16.6 - - - +
463A ALA 3.8 0.7 - - - -
465A LYS* 1.3 79.0 - - - +
467A CYS* 1.3 70.7 + - - +
468A ALA* 3.1 22.2 + - - -
551A LEU* 3.6 32.5 - - + +
553A ILE* 4.5 6.1 - - - -
570A VAL* 5.5 0.4 - - - -
447B LEU* 5.7 0.4 - - - -
448B SER 3.5 15.0 - - - +
449B ARG* 2.8 27.2 + - - +
454B VAL* 4.1 15.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il